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- PDB-7zx0: Crystal structure of Pol theta polymerase domain in complex with ... -

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基本情報

登録情報
データベース: PDB / ID: 7zx0
タイトルCrystal structure of Pol theta polymerase domain in complex with compound 5
要素
  • DNA (5'-D(*GP*CP*GP*GP*CP*TP*GP*TP*CP*AP*TP*TP*(DDG))-3')
  • DNA (5'-D(P*TP*TP*CP*CP*AP*AP*TP*GP*AP*CP*AP*GP*CP*CP*GP*C)-3')
  • DNA polymerase theta
キーワードTRANSFERASE / DNA polymerase / protein-DNA complex / DNA repair / inhibitor
機能・相同性
機能・相同性情報


double-strand break repair via alternative nonhomologous end joining / HDR through MMEJ (alt-NHEJ) / single-stranded DNA helicase activity / replication fork processing / mitochondrial nucleoid / site of DNA damage / 5'-deoxyribose-5-phosphate lyase activity / error-prone translesion synthesis / negative regulation of double-strand break repair via homologous recombination / somatic hypermutation of immunoglobulin genes ...double-strand break repair via alternative nonhomologous end joining / HDR through MMEJ (alt-NHEJ) / single-stranded DNA helicase activity / replication fork processing / mitochondrial nucleoid / site of DNA damage / 5'-deoxyribose-5-phosphate lyase activity / error-prone translesion synthesis / negative regulation of double-strand break repair via homologous recombination / somatic hypermutation of immunoglobulin genes / DNA helicase activity / protein homooligomerization / base-excision repair / RNA-directed DNA polymerase / RNA-directed DNA polymerase activity / double-strand break repair / site of double-strand break / DNA-directed DNA polymerase / DNA helicase / damaged DNA binding / DNA-directed DNA polymerase activity / DNA repair / DNA damage response / chromatin binding / magnesium ion binding / Golgi apparatus / ATP hydrolysis activity / nucleoplasm / ATP binding / identical protein binding / nucleus / cytosol
類似検索 - 分子機能
: / : / DNA_pol_Q helicase like region helical domain / Domain of unknown function (DUF7898) / DNA polymerase theta-like, helix-turn-helix domain / Helix-turn-helix domain / DNA polymerase A / DNA polymerase family A / DNA-directed DNA polymerase, family A, conserved site / DNA polymerase family A signature. ...: / : / DNA_pol_Q helicase like region helical domain / Domain of unknown function (DUF7898) / DNA polymerase theta-like, helix-turn-helix domain / Helix-turn-helix domain / DNA polymerase A / DNA polymerase family A / DNA-directed DNA polymerase, family A, conserved site / DNA polymerase family A signature. / DNA-directed DNA polymerase, family A, palm domain / DNA polymerase A domain / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Ribonuclease H superfamily / Ribonuclease H-like superfamily / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
類似検索 - ドメイン・相同性
2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE / Chem-K7X / DNA / DNA (> 10) / DNA polymerase theta
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
synthetic construct (人工物)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.99 Å
データ登録者Krajewski, W.W. / Turnbull, A.P. / Willis, S. / Charles, M. / Stockley, M. / Heald, R.A.
資金援助1件
組織認可番号国
Other private
引用ジャーナル: J.Med.Chem. / 年: 2022
タイトル: Discovery, Characterization, and Structure-Based Optimization of Small-Molecule In Vitro and In Vivo Probes for Human DNA Polymerase Theta.
著者: Stockley, M.L. / Ferdinand, A. / Benedetti, G. / Blencowe, P. / Boyd, S.M. / Calder, M. / Charles, M.D. / Edwardes, L.V. / Ekwuru, T. / Finch, H. / Galbiati, A. / Geo, L. / Grande, D. / ...著者: Stockley, M.L. / Ferdinand, A. / Benedetti, G. / Blencowe, P. / Boyd, S.M. / Calder, M. / Charles, M.D. / Edwardes, L.V. / Ekwuru, T. / Finch, H. / Galbiati, A. / Geo, L. / Grande, D. / Grinkevich, V. / Holliday, N.D. / Krajewski, W.W. / MacDonald, E. / Majithiya, J.B. / McCarron, H. / McWhirter, C.L. / Patel, V. / Pedder, C. / Rajendra, E. / Ranzani, M. / Rigoreau, L.J.M. / Robinson, H.M.R. / Schaedler, T. / Sirina, J. / Smith, G.C.M. / Swarbrick, M.E. / Turnbull, A.P. / Willis, S. / Heald, R.A.
履歴
登録2022年5月19日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02022年10月12日Provider: repository / タイプ: Initial release
改定 1.12022年10月19日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ASTM ..._citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title
改定 1.22022年11月9日Group: Database references / カテゴリ: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
改定 1.32024年1月31日Group: Data collection / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

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集合体

登録構造単位
AAA: DNA polymerase theta
BBB: DNA polymerase theta
CCC: DNA polymerase theta
DDD: DNA polymerase theta
EEE: DNA polymerase theta
FFF: DNA polymerase theta
GGG: DNA (5'-D(P*TP*TP*CP*CP*AP*AP*TP*GP*AP*CP*AP*GP*CP*CP*GP*C)-3')
HHH: DNA (5'-D(*GP*CP*GP*GP*CP*TP*GP*TP*CP*AP*TP*TP*(DDG))-3')
III: DNA (5'-D(P*TP*TP*CP*CP*AP*AP*TP*GP*AP*CP*AP*GP*CP*CP*GP*C)-3')
JJJ: DNA (5'-D(*GP*CP*GP*GP*CP*TP*GP*TP*CP*AP*TP*TP*(DDG))-3')
KKK: DNA (5'-D(P*TP*TP*CP*CP*AP*AP*TP*GP*AP*CP*AP*GP*CP*CP*GP*C)-3')
LLL: DNA (5'-D(*GP*CP*GP*GP*CP*TP*GP*TP*CP*AP*TP*TP*(DDG))-3')
MMM: DNA (5'-D(P*TP*TP*CP*CP*AP*AP*TP*GP*AP*CP*AP*GP*CP*CP*GP*C)-3')
NNN: DNA (5'-D(*GP*CP*GP*GP*CP*TP*GP*TP*CP*AP*TP*TP*(DDG))-3')
OOO: DNA (5'-D(P*TP*TP*CP*CP*AP*AP*TP*GP*AP*CP*AP*GP*CP*CP*GP*C)-3')
PPP: DNA (5'-D(*GP*CP*GP*GP*CP*TP*GP*TP*CP*AP*TP*TP*(DDG))-3')
QQQ: DNA (5'-D(P*TP*TP*CP*CP*AP*AP*TP*GP*AP*CP*AP*GP*CP*CP*GP*C)-3')
RRR: DNA (5'-D(*GP*CP*GP*GP*CP*TP*GP*TP*CP*AP*TP*TP*(DDG))-3')
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)547,13431
ポリマ－543,58518
非ポリマー3,54913
水181
1
AAA: DNA polymerase theta
GGG: DNA (5'-D(P*TP*TP*CP*CP*AP*AP*TP*GP*AP*CP*AP*GP*CP*CP*GP*C)-3')
HHH: DNA (5'-D(*GP*CP*GP*GP*CP*TP*GP*TP*CP*AP*TP*TP*(DDG))-3')
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)91,5696
ポリマ－90,5973
非ポリマー9723
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area6050 Å2
ΔGint-26 kcal/mol
Surface area29660 Å2
手法PISA
2
BBB: DNA polymerase theta
III: DNA (5'-D(P*TP*TP*CP*CP*AP*AP*TP*GP*AP*CP*AP*GP*CP*CP*GP*C)-3')
JJJ: DNA (5'-D(*GP*CP*GP*GP*CP*TP*GP*TP*CP*AP*TP*TP*(DDG))-3')
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)91,1135
ポリマ－90,5973
非ポリマー5152
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area5830 Å2
ΔGint-26 kcal/mol
Surface area29890 Å2
手法PISA
3
CCC: DNA polymerase theta
KKK: DNA (5'-D(P*TP*TP*CP*CP*AP*AP*TP*GP*AP*CP*AP*GP*CP*CP*GP*C)-3')
LLL: DNA (5'-D(*GP*CP*GP*GP*CP*TP*GP*TP*CP*AP*TP*TP*(DDG))-3')
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)91,1135
ポリマ－90,5973
非ポリマー5152
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area5950 Å2
ΔGint-24 kcal/mol
Surface area29860 Å2
手法PISA
4
DDD: DNA polymerase theta
MMM: DNA (5'-D(P*TP*TP*CP*CP*AP*AP*TP*GP*AP*CP*AP*GP*CP*CP*GP*C)-3')
NNN: DNA (5'-D(*GP*CP*GP*GP*CP*TP*GP*TP*CP*AP*TP*TP*(DDG))-3')
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)91,1135
ポリマ－90,5973
非ポリマー5152
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area6000 Å2
ΔGint-25 kcal/mol
Surface area29640 Å2
手法PISA
5
EEE: DNA polymerase theta
OOO: DNA (5'-D(P*TP*TP*CP*CP*AP*AP*TP*GP*AP*CP*AP*GP*CP*CP*GP*C)-3')
PPP: DNA (5'-D(*GP*CP*GP*GP*CP*TP*GP*TP*CP*AP*TP*TP*(DDG))-3')
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)91,1135
ポリマ－90,5973
非ポリマー5152
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area5900 Å2
ΔGint-25 kcal/mol
Surface area29780 Å2
手法PISA
6
FFF: DNA polymerase theta
QQQ: DNA (5'-D(P*TP*TP*CP*CP*AP*AP*TP*GP*AP*CP*AP*GP*CP*CP*GP*C)-3')
RRR: DNA (5'-D(*GP*CP*GP*GP*CP*TP*GP*TP*CP*AP*TP*TP*(DDG))-3')
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)91,1135
ポリマ－90,5973
非ポリマー5152
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area5780 Å2
ΔGint-25 kcal/mol
Surface area29660 Å2
手法PISA
単位格子
Length a, b, c (Å)59.050, 172.020, 288.610
Angle α, β, γ (deg.)90.000, 91.260, 90.000
Int Tables number4
Space group name H-MP1211
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11AAA
21BBB
32AAA
42CCC
53AAA
63DDD
74AAA
84EEE
95AAA
105FFF
116BBB
126CCC
137BBB
147DDD
158BBB
168EEE
179BBB
189FFF
1910CCC
2010DDD
2111CCC
2211EEE
2312CCC
2412FFF
2513DDD
2613EEE
2714DDD
2814FFF
2915EEE
3015FFF
3116GGG
3216III
3317GGG
3417KKK
3518GGG
3618MMM
3719GGG
3819OOO
3920GGG
4020QQQ
4121HHH
4221JJJ
4322HHH
4422LLL
4523HHH
4623NNN
4724HHH
4824PPP
4925HHH
5025RRR
5126III
5226KKK
5327III
5427MMM
5528III
5628OOO
5729III
5829QQQ
5930JJJ
6030LLL
6131JJJ
6231NNN
6332JJJ
6432PPP
6533JJJ
6633RRR
6734KKK
6834MMM
6935KKK
7035OOO
7136KKK
7236QQQ
7337LLL
7437NNN
7538LLL
7638PPP
7739LLL
7839RRR
7940MMM
8040OOO
8141MMM
8241QQQ
8342NNN
8442PPP
8543NNN
8643RRR
8744OOO
8844QQQ
8945PPP
9045RRR

NCSドメイン領域:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111SERSERVALVALAAAA1824 - 25905 - 726
211SERSERVALVALBBBB1824 - 25905 - 726
322SERSERVALVALAAAA1824 - 25905 - 726
422SERSERVALVALCCCC1824 - 25905 - 726
533SERSERVALVALAAAA1824 - 25905 - 726
633SERSERVALVALDDDD1824 - 25905 - 726
744SERSERVALVALAAAA1824 - 25905 - 726
844SERSERVALVALEEEE1824 - 25905 - 726
955SERSERVALVALAAAA1824 - 25905 - 726
1055SERSERVALVALFFFF1824 - 25905 - 726
1166SERSERVALVALBBBB1824 - 25905 - 726
1266SERSERVALVALCCCC1824 - 25905 - 726
1377SERSERVALVALBBBB1824 - 25905 - 726
1477SERSERVALVALDDDD1824 - 25905 - 726
1588SERSERVALVALBBBB1824 - 25905 - 726
1688SERSERVALVALEEEE1824 - 25905 - 726
1799SERSERVALVALBBBB1824 - 25905 - 726
1899SERSERVALVALFFFF1824 - 25905 - 726
191010SERSERVALVALCCCC1824 - 25905 - 726
201010SERSERVALVALDDDD1824 - 25905 - 726
211111SERSERVALVALCCCC1824 - 25905 - 726
221111SERSERVALVALEEEE1824 - 25905 - 726
231212SERSERVALVALCCCC1824 - 25905 - 726
241212SERSERVALVALFFFF1824 - 25905 - 726
251313SERSERVALVALDDDD1824 - 25905 - 726
261313SERSERVALVALEEEE1824 - 25905 - 726
271414SERSERVALVALDDDD1824 - 25905 - 726
281414SERSERVALVALFFFF1824 - 25905 - 726
291515SERSERVALVALEEEE1824 - 25905 - 726
301515SERSERVALVALFFFF1824 - 25905 - 726
311616DTDTDCDCGGGG2 - 171 - 16
321616DTDTDCDCIIII2 - 171 - 16
331717DTDTDCDCGGGG2 - 171 - 16
341717DTDTDCDCKKKK2 - 171 - 16
351818DTDTDCDCGGGG2 - 171 - 16
361818DTDTDCDCMMMM2 - 171 - 16
371919DTDTDCDCGGGG2 - 171 - 16
381919DTDTDCDCOOOO2 - 171 - 16
392020DTDTDCDCGGGG2 - 171 - 16
402020DTDTDCDCQQQQ2 - 171 - 16
412121DGDGDDGDDGHHHH1 - 131 - 13
422121DGDGDDGDDGJJJJ1 - 131 - 13
432222DGDGDDGDDGHHHH1 - 131 - 13
442222DGDGDDGDDGLLLL1 - 131 - 13
452323DGDGDDGDDGHHHH1 - 131 - 13
462323DGDGDDGDDGNNNN1 - 131 - 13
472424DGDGDDGDDGHHHH1 - 131 - 13
482424DGDGDDGDDGPPPP1 - 131 - 13
492525DGDGDDGDDGHHHH1 - 131 - 13
502525DGDGDDGDDGRRRR1 - 131 - 13
512626DTDTDCDCIIII2 - 171 - 16
522626DTDTDCDCKKKK2 - 171 - 16
532727DTDTDCDCIIII2 - 171 - 16
542727DTDTDCDCMMMM2 - 171 - 16
552828DTDTDCDCIIII2 - 171 - 16
562828DTDTDCDCOOOO2 - 171 - 16
572929DTDTDCDCIIII2 - 171 - 16
582929DTDTDCDCQQQQ2 - 171 - 16
593030DGDGDDGDDGJJJJ1 - 131 - 13
603030DGDGDDGDDGLLLL1 - 131 - 13
613131DGDGDDGDDGJJJJ1 - 131 - 13
623131DGDGDDGDDGNNNN1 - 131 - 13
633232DGDGDDGDDGJJJJ1 - 131 - 13
643232DGDGDDGDDGPPPP1 - 131 - 13
653333DGDGDDGDDGJJJJ1 - 131 - 13
663333DGDGDDGDDGRRRR1 - 131 - 13
673434DTDTDCDCKKKK2 - 171 - 16
683434DTDTDCDCMMMM2 - 171 - 16
693535DTDTDCDCKKKK2 - 171 - 16
703535DTDTDCDCOOOO2 - 171 - 16
713636DTDTDCDCKKKK2 - 171 - 16
723636DTDTDCDCQQQQ2 - 171 - 16
733737DGDGDDGDDGLLLL1 - 131 - 13
743737DGDGDDGDDGNNNN1 - 131 - 13
753838DGDGDDGDDGLLLL1 - 131 - 13
763838DGDGDDGDDGPPPP1 - 131 - 13
773939DGDGDDGDDGLLLL1 - 131 - 13
783939DGDGDDGDDGRRRR1 - 131 - 13
794040DTDTDCDCMMMM2 - 171 - 16
804040DTDTDCDCOOOO2 - 171 - 16
814141DTDTDCDCMMMM2 - 171 - 16
824141DTDTDCDCQQQQ2 - 171 - 16
834242DGDGDDGDDGNNNN1 - 131 - 13
844242DGDGDDGDDGPPPP1 - 131 - 13
854343DGDGDDGDDGNNNN1 - 131 - 13
864343DGDGDDGDDGRRRR1 - 131 - 13
874444DTDTDCDCOOOO2 - 171 - 16
884444DTDTDCDCQQQQ2 - 171 - 16
894545DGDGDDGDDGPPPP1 - 131 - 13
904545DGDGDDGDDGRRRR1 - 131 - 13

NCSアンサンブル:
ID詳細
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 3 4
3Local NCS retraints between domains: 5 6
4Local NCS retraints between domains: 7 8
5Local NCS retraints between domains: 9 10
6Local NCS retraints between domains: 11 12
7Local NCS retraints between domains: 13 14
8Local NCS retraints between domains: 15 16
9Local NCS retraints between domains: 17 18
10Local NCS retraints between domains: 19 20
11Local NCS retraints between domains: 21 22
12Local NCS retraints between domains: 23 24
13Local NCS retraints between domains: 25 26
14Local NCS retraints between domains: 27 28
15Local NCS retraints between domains: 29 30
16Local NCS retraints between domains: 31 32
17Local NCS retraints between domains: 33 34
18Local NCS retraints between domains: 35 36
19Local NCS retraints between domains: 37 38
20Local NCS retraints between domains: 39 40
21Local NCS retraints between domains: 41 42
22Local NCS retraints between domains: 43 44
23Local NCS retraints between domains: 45 46
24Local NCS retraints between domains: 47 48
25Local NCS retraints between domains: 49 50
26Local NCS retraints between domains: 51 52
27Local NCS retraints between domains: 53 54
28Local NCS retraints between domains: 55 56
29Local NCS retraints between domains: 57 58
30Local NCS retraints between domains: 59 60
31Local NCS retraints between domains: 61 62
32Local NCS retraints between domains: 63 64
33Local NCS retraints between domains: 65 66
34Local NCS retraints between domains: 67 68
35Local NCS retraints between domains: 69 70
36Local NCS retraints between domains: 71 72
37Local NCS retraints between domains: 73 74
38Local NCS retraints between domains: 75 76
39Local NCS retraints between domains: 77 78
40Local NCS retraints between domains: 79 80
41Local NCS retraints between domains: 81 82
42Local NCS retraints between domains: 83 84
43Local NCS retraints between domains: 85 86
44Local NCS retraints between domains: 87 88
45Local NCS retraints between domains: 89 90

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要素

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タンパク質 , 1種, 6分子 AAABBBCCCDDDEEEFFF

#1: タンパク質
DNA polymerase theta / DNA polymerase eta


分子量: 81771.719 Da / 分子数: 6 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: POLQ, POLH / プラスミド: pET21a / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): ROSETTA2(DE3)PLYSS / 参照: UniProt: O75417, DNA-directed DNA polymerase

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DNA鎖 , 2種, 12分子 GGGIIIKKKMMMOOOQQQHHHJJJLLLNNNPPPRRR

#2: DNA鎖
DNA (5'-D(P*TP*TP*CP*CP*AP*AP*TP*GP*AP*CP*AP*GP*CP*CP*GP*C)-3')


分子量: 4843.156 Da / 分子数: 6 / 由来タイプ: 合成 / 由来: (合成) synthetic construct (人工物)
#3: DNA鎖
DNA (5'-D(*GP*CP*GP*GP*CP*TP*GP*TP*CP*AP*TP*TP*(DDG))-3')


分子量: 3982.596 Da / 分子数: 6 / 由来タイプ: 合成 / 由来: (合成) synthetic construct (人工物)

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非ポリマー , 4種, 14分子

#4: 化合物
ChemComp-MG / MAGNESIUM ION / マグネシウムジカチオン


分子量: 24.305 Da / 分子数: 6 / 由来タイプ: 合成 / 式: Mg
#5: 化合物
ChemComp-DG3 / 2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE / ddGTP


分子量: 491.182 Da / 分子数: 6 / 由来タイプ: 合成 / 式: C10H16N5O12P3 / タイプ: SUBJECT OF INVESTIGATION
#6: 化合物 ChemComp-K7X / 2-[5-bromanyl-3-cyano-6-methyl-4-(trifluoromethyl)pyridin-2-yl]oxy-~{N}-ethyl-~{N}-(3-methylphenyl)ethanamide


分子量: 456.256 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C19H17BrF3N3O2 / タイプ: SUBJECT OF INVESTIGATION
#7: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 1 / 由来タイプ: 天然 / 式: H2O

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詳細

研究の焦点であるリガンドがあるかY

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実験情報

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実験

実験手法: X線回折 / 使用した結晶の数: 1

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試料調製

結晶マシュー密度: 2.7 Å3/Da / 溶媒含有率: 59.3 %
結晶化温度: 285 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 8.9
詳細: 15% (w/v) PEG 3350, 0.1 M Bis-Tris propane pH 8.9, 0.2 M sodium citrate tribasic dihydrate

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データ収集

回折平均測定温度: 100 K / Serial crystal experiment: N
放射光源由来: シンクロトロン / サイト: Diamond / ビームライン: I03 / 波長: 0.97623 Å
検出器タイプ: DECTRIS PILATUS 6M / 検出器: PIXEL / 日付: 2016年4月25日
放射プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長波長: 0.97623 Å / 相対比: 1
反射解像度: 2.93→147.75 Å / Num. obs: 122599 / % possible obs: 99.2 % / 冗長度: 3.4 % / CC1/2: 0.998 / Rrim(I) all: 0.084 / Net I/σ(I): 13.1
反射 シェル解像度: 2.93→3.01 Å / Num. unique obs: 9044 / CC1/2: 0.472 / Rrim(I) all: 1.169

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解析

ソフトウェア
名称バージョン分類
REFMAC5.8.0267精密化
xia2データ削減
xia2データスケーリング
PHASER位相決定
Cootモデル構築
精密化構造決定の手法: 分子置換
開始モデル: 7ZUS

7zus


解像度: 2.99→50.005 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.911 / WRfactor Rfree: 0.235 / WRfactor Rwork: 0.203 / SU B: 21.949 / SU ML: 0.386 / Average fsc free: 0.8642 / Average fsc work: 0.8744 / 交差検証法: FREE R-VALUE / ESU R Free: 0.42 / 詳細: Hydrogens have been added in their riding positions
Rfactor反射数%反射
Rfree0.2519 5815 5.04 %
Rwork0.218 109568 -
all0.22 --
obs-115383 99.149 %
溶媒の処理イオンプローブ半径: 0.8 Å / 減衰半径: 0.8 Å / VDWプローブ半径: 1.2 Å / 溶媒モデル: MASK BULK SOLVENT
原子変位パラメータBiso mean: 97.164 Å2
Baniso -1Baniso -2Baniso -3
1-5.623 Å20 Å20.246 Å2
2---4.446 Å2-0 Å2
3----1.187 Å2
精密化ステップサイクル: LAST / 解像度: 2.99→50.005 Å
タンパク質核酸リガンド溶媒全体
原子数29008 3528 214 1 32751
拘束条件
Refine-IDタイプDev idealDev ideal target数
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01333776
X-RAY DIFFRACTIONr_bond_other_d0.0010.01529643
X-RAY DIFFRACTIONr_ext_dist_refined_d0.0180.0151984
X-RAY DIFFRACTIONr_angle_refined_deg1.4381.65346532
X-RAY DIFFRACTIONr_angle_other_deg1.2361.57468073
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.43653773
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.72522.5551401
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.721154829
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.06815159
X-RAY DIFFRACTIONr_chiral_restr0.0830.24714
X-RAY DIFFRACTIONr_chiral_restr_other0.0250.25
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0235931
X-RAY DIFFRACTIONr_gen_planes_other0.0010.027389
X-RAY DIFFRACTIONr_nbd_refined0.2010.26261
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1790.226673
X-RAY DIFFRACTIONr_nbtor_refined0.1720.215898
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.215921
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.2459
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.040.213
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.230.229
X-RAY DIFFRACTIONr_nbd_other0.2890.288
X-RAY DIFFRACTIONr_mcbond_it7.74810.39915188
X-RAY DIFFRACTIONr_mcbond_other7.74810.39815187
X-RAY DIFFRACTIONr_mcangle_it12.0615.58418929
X-RAY DIFFRACTIONr_mcangle_other12.0615.58418930
X-RAY DIFFRACTIONr_scbond_it7.76811.00518588
X-RAY DIFFRACTIONr_scbond_other7.76611.00518585
X-RAY DIFFRACTIONr_scangle_it12.25116.42927603
X-RAY DIFFRACTIONr_scangle_other12.25216.42927601
X-RAY DIFFRACTIONr_lrange_it17.801211.49372337
X-RAY DIFFRACTIONr_lrange_other17.801211.49272338
X-RAY DIFFRACTIONr_ncsr_local_group_10.0280.0519981
X-RAY DIFFRACTIONr_ncsr_local_group_20.0260.0520268
X-RAY DIFFRACTIONr_ncsr_local_group_30.0350.0519943
X-RAY DIFFRACTIONr_ncsr_local_group_40.0270.0520093
X-RAY DIFFRACTIONr_ncsr_local_group_50.0260.0520117
X-RAY DIFFRACTIONr_ncsr_local_group_60.0210.0519953
X-RAY DIFFRACTIONr_ncsr_local_group_70.0320.0519742
X-RAY DIFFRACTIONr_ncsr_local_group_80.020.0520030
X-RAY DIFFRACTIONr_ncsr_local_group_90.0180.0519923
X-RAY DIFFRACTIONr_ncsr_local_group_100.0320.0519919
X-RAY DIFFRACTIONr_ncsr_local_group_110.0240.0520054
X-RAY DIFFRACTIONr_ncsr_local_group_120.0210.0520100
X-RAY DIFFRACTIONr_ncsr_local_group_130.0260.0519849
X-RAY DIFFRACTIONr_ncsr_local_group_140.0270.0519963
X-RAY DIFFRACTIONr_ncsr_local_group_150.0160.0520009
X-RAY DIFFRACTIONr_ncsr_local_group_160.0170.051260
X-RAY DIFFRACTIONr_ncsr_local_group_170.0080.051265
X-RAY DIFFRACTIONr_ncsr_local_group_180.0120.051266
X-RAY DIFFRACTIONr_ncsr_local_group_190.0110.051263
X-RAY DIFFRACTIONr_ncsr_local_group_200.010.051263
X-RAY DIFFRACTIONr_ncsr_local_group_210.0140.051152
X-RAY DIFFRACTIONr_ncsr_local_group_220.0070.051157
X-RAY DIFFRACTIONr_ncsr_local_group_230.0090.051158
X-RAY DIFFRACTIONr_ncsr_local_group_240.0090.051156
X-RAY DIFFRACTIONr_ncsr_local_group_250.0080.051153
X-RAY DIFFRACTIONr_ncsr_local_group_260.0140.051262
X-RAY DIFFRACTIONr_ncsr_local_group_270.0150.051263
X-RAY DIFFRACTIONr_ncsr_local_group_280.0120.051260
X-RAY DIFFRACTIONr_ncsr_local_group_290.0120.051262
X-RAY DIFFRACTIONr_ncsr_local_group_300.0140.051153
X-RAY DIFFRACTIONr_ncsr_local_group_310.0130.051151
X-RAY DIFFRACTIONr_ncsr_local_group_320.0090.051153
X-RAY DIFFRACTIONr_ncsr_local_group_330.010.051153
X-RAY DIFFRACTIONr_ncsr_local_group_340.0080.051265
X-RAY DIFFRACTIONr_ncsr_local_group_350.0070.051264
X-RAY DIFFRACTIONr_ncsr_local_group_360.0070.051265
X-RAY DIFFRACTIONr_ncsr_local_group_370.0070.051155
X-RAY DIFFRACTIONr_ncsr_local_group_380.0080.051155
X-RAY DIFFRACTIONr_ncsr_local_group_390.0060.051154
X-RAY DIFFRACTIONr_ncsr_local_group_400.010.051264
X-RAY DIFFRACTIONr_ncsr_local_group_410.0090.051266
X-RAY DIFFRACTIONr_ncsr_local_group_420.0080.051155
X-RAY DIFFRACTIONr_ncsr_local_group_430.0070.051153
X-RAY DIFFRACTIONr_ncsr_local_group_440.0060.051263
X-RAY DIFFRACTIONr_ncsr_local_group_450.0050.051154
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDタイプRms dev position (Å)Weight position
11AAAX-RAY DIFFRACTIONLocal ncs0.027510.05009
12BBBX-RAY DIFFRACTIONLocal ncs0.027510.05009
23AAAX-RAY DIFFRACTIONLocal ncs0.026150.05009
24CCCX-RAY DIFFRACTIONLocal ncs0.026150.05009
35AAAX-RAY DIFFRACTIONLocal ncs0.035250.05009
36DDDX-RAY DIFFRACTIONLocal ncs0.035250.05009
47AAAX-RAY DIFFRACTIONLocal ncs0.02650.05009
48EEEX-RAY DIFFRACTIONLocal ncs0.02650.05009
59AAAX-RAY DIFFRACTIONLocal ncs0.025960.05009
510FFFX-RAY DIFFRACTIONLocal ncs0.025960.05009
611BBBX-RAY DIFFRACTIONLocal ncs0.021030.05009
612CCCX-RAY DIFFRACTIONLocal ncs0.021030.05009
713BBBX-RAY DIFFRACTIONLocal ncs0.032280.05009
714DDDX-RAY DIFFRACTIONLocal ncs0.032280.05009
815BBBX-RAY DIFFRACTIONLocal ncs0.020320.05009
816EEEX-RAY DIFFRACTIONLocal ncs0.020320.05009
917BBBX-RAY DIFFRACTIONLocal ncs0.017550.05009
918FFFX-RAY DIFFRACTIONLocal ncs0.017550.05009
1019CCCX-RAY DIFFRACTIONLocal ncs0.032020.05009
1020DDDX-RAY DIFFRACTIONLocal ncs0.032020.05009
1121CCCX-RAY DIFFRACTIONLocal ncs0.023660.05009
1122EEEX-RAY DIFFRACTIONLocal ncs0.023660.05009
1223CCCX-RAY DIFFRACTIONLocal ncs0.02070.05009
1224FFFX-RAY DIFFRACTIONLocal ncs0.02070.05009
1325DDDX-RAY DIFFRACTIONLocal ncs0.026440.05009
1326EEEX-RAY DIFFRACTIONLocal ncs0.026440.05009
1427DDDX-RAY DIFFRACTIONLocal ncs0.02750.05009
1428FFFX-RAY DIFFRACTIONLocal ncs0.02750.05009
1529EEEX-RAY DIFFRACTIONLocal ncs0.01640.05009
1530FFFX-RAY DIFFRACTIONLocal ncs0.01640.05009
1631GGGX-RAY DIFFRACTIONLocal ncs0.01730.05011
1632IIIX-RAY DIFFRACTIONLocal ncs0.01730.05011
1733GGGX-RAY DIFFRACTIONLocal ncs0.007990.05011
1734KKKX-RAY DIFFRACTIONLocal ncs0.007990.05011
1835GGGX-RAY DIFFRACTIONLocal ncs0.011510.05011
1836MMMX-RAY DIFFRACTIONLocal ncs0.011510.05011
1937GGGX-RAY DIFFRACTIONLocal ncs0.010640.05011
1938OOOX-RAY DIFFRACTIONLocal ncs0.010640.05011
2039GGGX-RAY DIFFRACTIONLocal ncs0.010060.05011
2040QQQX-RAY DIFFRACTIONLocal ncs0.010060.05011
2141HHHX-RAY DIFFRACTIONLocal ncs0.013760.0501
2142JJJX-RAY DIFFRACTIONLocal ncs0.013760.0501
2243HHHX-RAY DIFFRACTIONLocal ncs0.007260.0501
2244LLLX-RAY DIFFRACTIONLocal ncs0.007260.0501
2345HHHX-RAY DIFFRACTIONLocal ncs0.009040.05011
2346NNNX-RAY DIFFRACTIONLocal ncs0.009040.05011
2447HHHX-RAY DIFFRACTIONLocal ncs0.009310.0501
2448PPPX-RAY DIFFRACTIONLocal ncs0.009310.0501
2549HHHX-RAY DIFFRACTIONLocal ncs0.008480.0501
2550RRRX-RAY DIFFRACTIONLocal ncs0.008480.0501
2651IIIX-RAY DIFFRACTIONLocal ncs0.014190.05011
2652KKKX-RAY DIFFRACTIONLocal ncs0.014190.05011
2753IIIX-RAY DIFFRACTIONLocal ncs0.015420.05011
2754MMMX-RAY DIFFRACTIONLocal ncs0.015420.05011
2855IIIX-RAY DIFFRACTIONLocal ncs0.011530.05011
2856OOOX-RAY DIFFRACTIONLocal ncs0.011530.05011
2957IIIX-RAY DIFFRACTIONLocal ncs0.01230.05011
2958QQQX-RAY DIFFRACTIONLocal ncs0.01230.05011
3059JJJX-RAY DIFFRACTIONLocal ncs0.01360.0501
3060LLLX-RAY DIFFRACTIONLocal ncs0.01360.0501
3161JJJX-RAY DIFFRACTIONLocal ncs0.012570.0501
3162NNNX-RAY DIFFRACTIONLocal ncs0.012570.0501
3263JJJX-RAY DIFFRACTIONLocal ncs0.009480.0501
3264PPPX-RAY DIFFRACTIONLocal ncs0.009480.0501
3365JJJX-RAY DIFFRACTIONLocal ncs0.010280.0501
3366RRRX-RAY DIFFRACTIONLocal ncs0.010280.0501
3467KKKX-RAY DIFFRACTIONLocal ncs0.007990.05011
3468MMMX-RAY DIFFRACTIONLocal ncs0.007990.05011
3569KKKX-RAY DIFFRACTIONLocal ncs0.00720.05011
3570OOOX-RAY DIFFRACTIONLocal ncs0.00720.05011
3671KKKX-RAY DIFFRACTIONLocal ncs0.006750.05011
3672QQQX-RAY DIFFRACTIONLocal ncs0.006750.05011
3773LLLX-RAY DIFFRACTIONLocal ncs0.007290.0501
3774NNNX-RAY DIFFRACTIONLocal ncs0.007290.0501
3875LLLX-RAY DIFFRACTIONLocal ncs0.007660.0501
3876PPPX-RAY DIFFRACTIONLocal ncs0.007660.0501
3977LLLX-RAY DIFFRACTIONLocal ncs0.006430.0501
3978RRRX-RAY DIFFRACTIONLocal ncs0.006430.0501
4079MMMX-RAY DIFFRACTIONLocal ncs0.009550.05011
4080OOOX-RAY DIFFRACTIONLocal ncs0.009550.05011
4181MMMX-RAY DIFFRACTIONLocal ncs0.009390.05011
4182QQQX-RAY DIFFRACTIONLocal ncs0.009390.05011
4283NNNX-RAY DIFFRACTIONLocal ncs0.008080.0501
4284PPPX-RAY DIFFRACTIONLocal ncs0.008080.0501
4385NNNX-RAY DIFFRACTIONLocal ncs0.007350.0501
4386RRRX-RAY DIFFRACTIONLocal ncs0.007350.0501
4487OOOX-RAY DIFFRACTIONLocal ncs0.006240.05011
4488QQQX-RAY DIFFRACTIONLocal ncs0.006240.05011
4589PPPX-RAY DIFFRACTIONLocal ncs0.005180.0501
4590RRRX-RAY DIFFRACTIONLocal ncs0.005180.0501
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.99-3.0670.3564260.34481030.34585490.6130.63499.76610.323
3.067-3.1510.3483740.32679120.32783060.7110.72299.75920.298
3.151-3.2420.3023930.28777270.28781460.8170.81299.68080.257
3.242-3.3410.2774100.25574120.25678320.8620.8799.87230.224
3.341-3.450.2973840.25372990.25576950.8520.87999.84410.225
3.45-3.5710.2813860.2469370.24273400.8760.89599.76840.214
3.571-3.7050.2764030.24167700.24371860.8830.89399.81910.215
3.705-3.8550.2493170.2264670.22168070.9080.91399.66210.197
3.855-4.0260.2413400.20662240.20866030.920.92499.40940.184
4.026-4.2210.2483170.20259930.20463570.9070.92599.26070.185
4.221-4.4470.2182720.17956000.18159360.9360.94598.92180.168
4.447-4.7150.2063140.16952720.17156720.9450.95398.48380.16
4.715-5.0370.2032940.17449900.17653740.9420.94998.32530.167
5.037-5.4360.2352450.1846620.18349830.9340.9598.47480.173
5.436-5.9480.2792330.22243020.22546070.9010.92198.43720.211
5.948-6.6390.2561890.23438790.23541620.9030.91897.74150.227
6.639-7.6430.2461700.2134180.21236700.9160.92997.76570.21
7.643-9.3070.2171510.18429110.18631350.9460.95397.67140.197
9.307-12.9390.2091250.19522880.19624770.9470.95497.41620.215
12.939-50.0050.345690.29513700.29814730.8370.88697.69180.321

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万見について

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お知らせ

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2022年2月9日: EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

  • EMDBのヘッダファイルのバージョン3が、公式のフォーマットとなりました。
  • これまでは公式だったバージョン1.9は、アーカイブから削除されます。

関連情報:EMDBヘッダ

外部リンク:wwPDBはEMDBデータモデルのバージョン3へ移行します

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2020年8月12日: 新型コロナ情報

新型コロナ情報

URL: https://pdbj.org/emnavi/covid19.php

新ページ: EM Navigatorに新型コロナウイルスの特設ページを開設しました。

関連情報:Covid-19情報 / 2020年3月5日: 新型コロナウイルスの構造データ

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2020年3月5日: 新型コロナウイルスの構造データ

新型コロナウイルスの構造データ

関連情報:万見生物種 / 2020年8月12日: 新型コロナ情報

外部リンク:COVID-19特集ページ - PDBj / 今月の分子2020年2月：コロナウイルスプロテーアーゼ

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2019年1月31日: EMDBのIDの桁数の変更

EMDBのIDの桁数の変更

  • EMDBエントリに付与されているアクセスコード(EMDB-ID)は4桁の数字(例、EMD-1234)でしたが、間もなく枯渇します。これまでの4桁のID番号は4桁のまま変更されませんが、4桁の数字を使い切った後に発行されるIDは5桁以上の数字(例、EMD-12345)になります。5桁のIDは2019年の春頃から発行される見通しです。
  • EM Navigator/万見では、接頭語「EMD-」は省略されています。

関連情報:Q: 「EMD」とは何ですか？ / 万見/EM NavigatorにおけるID/アクセスコードの表記

外部リンク:EMDB Accession Codes are Changing Soon! / PDBjへお問い合わせ

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2017年7月12日: PDB大規模アップデート

PDB大規模アップデート

  • 新バージョンのPDBx/mmCIF辞書形式に基づくデータがリリースされました。
  • 今回の更新はバージョン番号が4から5になる大規模なもので、全エントリデータの書き換えが行われる「Remediation」というアップデートに該当します。
  • このバージョンアップで、電子顕微鏡の実験手法に関する多くの項目の書式が改定されました(例：em_softwareなど)。
  • EM NavigatorとYorodumiでも、この改定に基づいた表示内容になります。

外部リンク:wwPDB Remediation / OneDepデータ基準に準拠した、より強化された内容のモデル構造ファイルが、PDBアーカイブで公開されました。

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万見 (Yorodumi)

幾万の構造データを、幾万の視点から

  • 万見(Yorodumi)は、EMDB/PDB/SASBDBなどの構造データを閲覧するためのページです。
  • EM Navigatorの詳細ページの後継、Omokage検索のフロントエンドも兼ねています。

関連情報:EMDB / PDB / SASBDB / 3つのデータバンクの比較 / 万見検索 / 2016年8月31日: 新しいEM Navigatorと万見 / 万見文献 / Jmol/JSmol / 機能・相同性情報 / 新しいEM Navigatorと万見の変更点

他の情報も見る